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  1. Article ; Online: A Framework for Comparison and Assessment of Synthetic RNA-Seq Data.

    Shakola, Felitsiya / Palejev, Dean / Ivanov, Ivan

    Genes

    2022  Volume 13, Issue 12

    Abstract: The ever-growing number of methods for the generation of synthetic bulk and single cell RNA-seq data have multiple and diverse applications. They are often aimed at benchmarking bioinformatics algorithms for purposes such as sample classification, ... ...

    Abstract The ever-growing number of methods for the generation of synthetic bulk and single cell RNA-seq data have multiple and diverse applications. They are often aimed at benchmarking bioinformatics algorithms for purposes such as sample classification, differential expression analysis, correlation and network studies and the optimization of data integration and normalization techniques. Here, we propose a general framework to compare synthetically generated RNA-seq data and select a data-generating tool that is suitable for a set of specific study goals. As there are multiple methods for synthetic RNA-seq data generation, researchers can use the proposed framework to make an informed choice of an RNA-seq data simulation algorithm and software that are best suited for their specific scientific questions of interest.
    Language English
    Publishing date 2022-12-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13122362
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: A Framework for Comparison and Assessment of Synthetic RNA-Seq Data

    Shakola, Felitsiya / Palejev, Dean / Ivanov, Ivan

    Genes (Basel). 2022 Dec. 14, v. 13, no. 12

    2022  

    Abstract: The ever-growing number of methods for the generation of synthetic bulk and single cell RNA-seq data have multiple and diverse applications. They are often aimed at benchmarking bioinformatics algorithms for purposes such as sample classification, ... ...

    Abstract The ever-growing number of methods for the generation of synthetic bulk and single cell RNA-seq data have multiple and diverse applications. They are often aimed at benchmarking bioinformatics algorithms for purposes such as sample classification, differential expression analysis, correlation and network studies and the optimization of data integration and normalization techniques. Here, we propose a general framework to compare synthetically generated RNA-seq data and select a data-generating tool that is suitable for a set of specific study goals. As there are multiple methods for synthetic RNA-seq data generation, researchers can use the proposed framework to make an informed choice of an RNA-seq data simulation algorithm and software that are best suited for their specific scientific questions of interest.
    Keywords algorithms ; bioinformatics ; computer software ; gene expression regulation ; sequence analysis
    Language English
    Dates of publication 2022-1214
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes13122362
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: A rare case of

    Mermeklieva, Elena / Kamenarova, Kunka / Mihova, Kalina / Shakola, Felitsiya / Kaneva, Radka

    Ophthalmic genetics

    2021  Volume 42, Issue 6, Page(s) 747–752

    Abstract: Aim: To present a rare clinical case of : Material and methods: A 26-year-old woman underwent detailed ophthalmic examinationincluding fundus photography, full-field and multifocal electroretinography, visual field testing, optical coherence ... ...

    Abstract Aim: To present a rare clinical case of
    Material and methods: A 26-year-old woman underwent detailed ophthalmic examinationincluding fundus photography, full-field and multifocal electroretinography, visual field testing, optical coherence tomography and fluorescein angiography, which established the clinical diagnosis. Next-generation sequencing of a custom panel including 140 of the most common genes for inherited retinal degenerations was used for mutation screening.
    Results: The symptoms onset was two years ago included gradual loss of vision and photophobia. The clinical findings were reduced visual acuity, central and peripheral scotomas, sporadic pigmentary cells localized mainly in the peripheral retina, a thinner retina in the macula and peripherally, moderate retinal vessels attenuation and reduced cone and rod ERG responses. The genetic analysisfound that the patient was homozygous for two already reported mutations:
    Conclusion: The rare haplotype of
    MeSH term(s) Adult ; Bulgaria/epidemiology ; Cadherin Related Proteins/genetics ; Cone-Rod Dystrophies/diagnostic imaging ; Cone-Rod Dystrophies/epidemiology ; Cone-Rod Dystrophies/genetics ; Cone-Rod Dystrophies/physiopathology ; DNA Mutational Analysis ; Electroretinography ; Eye Proteins/genetics ; Female ; Fluorescein Angiography ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Mutation/genetics ; Nerve Tissue Proteins/genetics ; Pedigree ; Receptors, G-Protein-Coupled/genetics ; Retina/physiopathology ; Tomography, Optical Coherence ; Visual Acuity/physiology ; Visual Field Tests ; Visual Fields/physiology
    Chemical Substances CDHR1 protein, human ; Cadherin Related Proteins ; Eye Proteins ; G protein-coupled receptor RGR ; Nerve Tissue Proteins ; Receptors, G-Protein-Coupled
    Language English
    Publishing date 2021-07-06
    Publishing country England
    Document type Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1199279-7
    ISSN 1744-5094 ; 0167-6784 ; 1381-6810
    ISSN (online) 1744-5094
    ISSN 0167-6784 ; 1381-6810
    DOI 10.1080/13816810.2021.1946700
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1708: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  4. Article ; Online: A pilot study reveals the potential of miR-31-3p and miR-196a-5p as non-invasive biomarkers in advanced laryngeal cancer.

    Kyurkchiyan, Silva Garo / Popov, Todor Miroslavov / Shakola, Felitsiya / Rangachev, Julian / Mitev, Vanyo Ivanov / Kaneva, Radka

    Folia medica

    2021  Volume 63, Issue 3, Page(s) 355–364

    Abstract: Introduction: Recently, miRNAs have become popular molecules used as non-invasive biomarkers in cancer diseases.: Aim: The aim of the study was to explore the expression of four miRNAs isoforms: miR-31-3p, miR-196a-5p, miR-210-3p and miR-424-5p in ... ...

    Abstract Introduction: Recently, miRNAs have become popular molecules used as non-invasive biomarkers in cancer diseases.
    Aim: The aim of the study was to explore the expression of four miRNAs isoforms: miR-31-3p, miR-196a-5p, miR-210-3p and miR-424-5p in plasma and tissue samples from patients with advanced laryngeal squamous cell carcinoma (LSCC) and healthy controls.
    Materials and methods: Fresh-frozen tumour and normal laryngeal tissue as well as plasma samples were obtained from 22 patients diagnosed with advanced LSCC. The control group included plasma samples from 21 cancer-free volunteers. Total RNA (including miRNAs) extraction, reverse transcription and real time qPCR were the laboratory techniques used in the study. The obtained results were analyzed using SPSS software v. 23.
    Results: We found that miR-31-3p, miR-196a-5p, and miR-210-3p levels were significantly elevated in laryngeal tumour tissue, but only the levels of miR-31-3p and miR-196a-5p were significantly upregulated in the plasma LSCC target group. Positive correlation was obtained for miR-31-3p (rs=0.443, p=0.039) and miR-196a-5p (rs=0.548; p=0.008) between plasma and adjacent tumour tissue LSCC samples. ROC analyses were used to evaluate the discriminative power of both miRNAs alone and in combination. The combination of miR-31-3p and miR-196a-5p showed best results with AUC=0.978 (95% CI: 0.945-1.000, p.
    MeSH term(s) Biomarkers, Tumor/genetics ; Humans ; Laryngeal Neoplasms/genetics ; MicroRNAs/genetics ; MicroRNAs/supply & distribution ; Pilot Projects ; Squamous Cell Carcinoma of Head and Neck
    Chemical Substances Biomarkers, Tumor ; MIRN31 microRNA, human ; MicroRNAs
    Language English
    Publishing date 2021-07-01
    Publishing country Bulgaria
    Document type Journal Article
    ZDB-ID 300275-5
    ISSN 1314-2143 ; 0430-8638 ; 0204-8043
    ISSN (online) 1314-2143
    ISSN 0430-8638 ; 0204-8043
    DOI 10.3897/folmed.63.e55346
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 972: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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  5. Article ; Online: Splicing Regulation of Pro-Inflammatory Cytokines and Chemokines: At the Interface of the Neuroendocrine and Immune Systems.

    Shakola, Felitsiya / Suri, Parul / Ruggiu, Matteo

    Biomolecules

    2015  Volume 5, Issue 3, Page(s) 2073–2100

    Abstract: Alternative splicing plays a key role in posttranscriptional regulation of gene expression, allowing a single gene to encode multiple protein isoforms. As such, alternative splicing amplifies the coding capacity of the genome enormously, generates ... ...

    Abstract Alternative splicing plays a key role in posttranscriptional regulation of gene expression, allowing a single gene to encode multiple protein isoforms. As such, alternative splicing amplifies the coding capacity of the genome enormously, generates protein diversity, and alters protein function. More than 90% of human genes undergo alternative splicing, and alternative splicing is especially prevalent in the nervous and immune systems, tissues where cells need to react swiftly and adapt to changes in the environment through carefully regulated mechanisms of cell differentiation, migration, targeting, and activation. Given its prevalence and complexity, this highly regulated mode of gene expression is prone to be affected by disease. In the following review, we look at how alternative splicing of signaling molecules—cytokines and their receptors—changes in different pathological conditions, from chronic inflammation to neurologic disorders, providing means of functional interaction between the immune and neuroendocrine systems. Switches in alternative splicing patterns can be very dynamic and can produce signaling molecules with distinct or antagonistic functions and localization to different subcellular compartments. This newly discovered link expands our understanding of the biology of immune and neuroendocrine cells, and has the potential to open new windows of opportunity for treatment of neurodegenerative disorders.
    MeSH term(s) Alternative Splicing ; Animals ; Cytokines/genetics ; Humans ; Immune System ; Inflammation/genetics ; Inflammation/immunology ; Neurodegenerative Diseases/genetics ; Neurodegenerative Diseases/immunology ; Neuroprotection/genetics ; Neuroprotection/immunology ; Neurosecretory Systems
    Chemical Substances Cytokines
    Language English
    Publishing date 2015-09-07
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2701262-1
    ISSN 2218-273X ; 2218-273X
    ISSN (online) 2218-273X
    ISSN 2218-273X
    DOI 10.3390/biom5032073
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Radiolabeled semi-quantitative RT-PCR assay for the analysis of alternative splicing of interleukin genes.

    Shakola, Felitsiya / Byrne, Stephen / Javed, Kainaat / Ruggiu, Matteo

    Methods in molecular biology (Clifton, N.J.)

    2014  Volume 1172, Page(s) 343–362

    Abstract: Alternative splicing evolved as a very efficient way to generate proteome diversity from a limited number of genes, while at the same time modulating posttranscriptional events of gene expression-such as stability, turnover, subcellular localization, ... ...

    Abstract Alternative splicing evolved as a very efficient way to generate proteome diversity from a limited number of genes, while at the same time modulating posttranscriptional events of gene expression-such as stability, turnover, subcellular localization, binding properties, and general activity of both mRNAs and proteins. Since the vast majority of human genes undergo alternative splicing, it comes to no surprise that interleukin genes also show extensive alternative splicing. In fact, there is a growing body of evidence indicating that alternative splicing plays a central role in modulating the pleiotropic functions of cytokines, and aberrant expression of alternatively spliced interleukin mRNAs has been linked to disease. However, while several interleukin splice variants have been described, their function is still poorly understood. This is particularly relevant, since alternatively spliced cytokine isoforms can act both as disease biomarkers and as candidate entry points for therapeutic intervention. In this chapter we describe a protocol that uses radiolabeled semi-quantitative RT-PCR to efficiently detect, analyze, and quantify alternative splicing patterns of cytokine genes.
    MeSH term(s) Adenosine Triphosphate/metabolism ; Alternative Splicing ; Cell Line ; DNA Primers ; Electrophoresis, Polyacrylamide Gel ; Humans ; Interleukin-7/genetics ; Interleukin-7/metabolism ; Leukocytes, Mononuclear/cytology ; Leukocytes, Mononuclear/metabolism ; Neural Stem Cells/cytology ; Neural Stem Cells/metabolism ; Phosphorus Radioisotopes ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; RNA Splice Sites ; Reverse Transcriptase Polymerase Chain Reaction/methods
    Chemical Substances DNA Primers ; IL7 protein, human ; Interleukin-7 ; Phosphorus Radioisotopes ; Protein Isoforms ; RNA Splice Sites ; Adenosine Triphosphate (8L70Q75FXE)
    Language English
    Publishing date 2014
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-0928-5_31
    Database MEDical Literature Analysis and Retrieval System OnLINE

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